Methods of generating nucleic acid fragments

ABSTRACT

Provided herein are methods of using a Cas1 polypeptide to generate nucleic fragments from a DNA substrate. These methods may be performed in vitro or in vivo. Also provided are methods of screening for modulators of Cas1.

CROSS-REFERENCE

This application claims the benefit of U.S. Provisional PatentApplication No. 61/312,510, filed Mar. 10, 2010, which application isincorporated herein by reference in its entirety.

BACKGROUND

Nucleases are enzymes that degrade nucleic acids (e.g., deoxyribonucleicacids, DNA, and ribonucleic acids, RNA) and exist in various biologicalmaterials. These enzymes are involved in DNA and RNA metabolism,including degradation, synthesis and genetic recombination of nucleicacids. Nucleases are generally classified into exonucleases andendonucleases according to their mode of action. The former type acts onthe terminus of a nucleic acid molecule and hydrolyzes the chainprogressively to liberate nucleotides, while the latter type cleaves aphosphodiester bond in a nucleic acid molecule distributively to produceDNA or RNA fragments or oligonucleotides.

Deoxyribonucleases (DNases) are phosphodiesterases capable ofhydrolyzing polydeoxyribonucleic acid. DNases have been purified fromvarious species to various degrees. Among other uses, DNases find use asreagents in a variety of protocols in molecular biology. DNases havealso been used for therapeutic purposes, for example, to reduce theviscosity of pulmonary secretions in such diseases as pneumonia andcystic fibrosis, thereby aiding in the clearing of respiratory airways.

LITERATURE

Makarova et al. (2002) Nucleic Acids Res 30:482-496; Makarova et al.(2006) Biology Direct 1:1-26; Wiedenheft et al. (2009) Structure 17:904.

SUMMARY

The present disclosure provides methods of using a Cas1 polypeptide togenerate nucleic fragments from a DNA substrate. These methods may beused in vitro or in vivo. Also provided are methods of screening formodulators of Cas1.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts crystal structure of the Cas1 protein from Pseudomonasaeruginosa.

FIGS. 2A-2C depict two different orientations and two distinct folds inthe β-strand domain of Cas1 from P. aeruginosa. Panel A depictssuperimposition of the C-terminal α-helical domains of molecules A andC. Panel B depicts a view down the barrel of α8. Panel C illustratesthat superimposing the β-strand domains for molecule A and C highlightstwo structural differences.

FIGS. 3A and 3B depict dimerization of the Cas1 protein from P.aeruginosa. Panel A depicts a ribbon diagram of Cas1 homodimer withmolecule A shown in grey and molecule C shown in light blue. Panel Bshows a view down the dimer interface.

FIGS. 4A-4C provide a schematic of the structural comparison of the Cas1proteins from P. aeruginosa and A. aeolicus. Panel A shows molecule Afrom PaCas1 (in grey) superimposed on molecule A from AaCas1 (lightgreen). Panel B depict superposition of the α-helical domains of PaCas1and AaCas1, as viewed from the perspective of the β-strand domain. PanelC depict the β-strand domains of these two molecules.

FIGS. 5A-5D illustrate that Cas1 is a DNA-specific endonuclease. Panel Ashows that Cas1 nuclease activity is restricted to DNA substrates. PanelB depicts the time course of Cas 1 nuclease activity on four distinctdsDNA substrates. Panel C depicts the time course of Cas1 nucleaseactivity on linear dsDNA substrate. Panel D illustrates that Cas1 is anendonuclease.

FIGS. 6A-6C illustrate that Cas1 is a metal-dependent nuclease. Panel Aillustrates that manganese supports Cas1 mediated non-specific nucleaseactivity. Panel B shows that the metal preference of Cas1 is saltdependent. Panel C shows that Cas1 mediated cleavage of ssDNA issupported exclusively by manganese.

FIGS. 7A-7D illustrate that mutants of conserved residues in the metalbinding pocket of Cas1 inhibit nuclease activity. Panel A shows aclose-up of the metal binding pocket in the α-helical domain of moleculeA. Panel B shows SDS-PAGE of the purified Cas1 and Cas1 mutants. Panel Cdepicts nuclease activity assay for Cas1 and Cas1 mutants.

FIGS. 8A and 8B depict Cas1 protein structure from A. aeolicus. Panel Ashows the superimposition of molecules A (green) and B (pink) of AaCas1.Panel B shows a dimer formed from molecules A (green) and B (pink) ofAaCas1.

FIGS. 9A to 9F depict Cas1 amino acid sequences (SEQ ID NOs:1-21).

FIG. 10 depicts an amino acid sequence of a Pseudomonas aeruginosa Cas1polypeptide (SEQ ID NO:22).

DEFINITIONS

The term “biofilm” as used herein refers to an aggregate ofmicroorganisms in which the microorganisms adhere to one another and/orto a surface. Such microorganisms can be embedded within a self-producedmatrix of extracellular polymeric substance (EPS). Biofilm EPS, which isalso referred to as “slime”, is a mixture of extracellular DNA,proteins, and polysaccharides. Biofilms may form on living or non-livingsurfaces, and represent a prevalent mode of microbial life in natural,industrial and hospital settings.

“Reducing or inhibiting” in reference to a biofilm refers to theprevention of biofilm formation or growth, reduction in the rate ofbiofilm formation or growth, partial or complete inhibition of biofilmformation or growth.

Before the present invention is further described, it is to beunderstood that this invention is not limited to particular embodimentsdescribed, as such may, of course, vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to be limiting, sincethe scope of the present invention will be limited only by the appendedclaims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges, and are also encompassed within the invention, subjectto any specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, the preferredmethods and materials are now described. All publications mentionedherein are incorporated herein by reference to disclose and describe themethods and/or materials in connection with which the publications arecited.

It must be noted that and in the appended claims, the singular forms“a,” “an,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a method” includesa plurality of such methods and equivalents thereof known to thoseskilled in the art, and so forth. It is further noted that the claimsmay be drafted to exclude any optional element. As such, this statementis intended to serve as antecedent basis for use of such exclusiveterminology as “solely,” “only” and the like in connection with therecitation of claim elements, or use of a “negative” limitation.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

DETAILED DESCRIPTION

Provided herein are methods of using Cas1 to generate nucleic fragmentsfrom a DNA substrate. These methods may be used in vitro or in vivo.Also provided are methods of screening for modulators of Cas1.

METHODS OF GENERATING NUCLEIC ACID FRAGMENTS

The present disclosure provides methods for generating nucleic acidfragments of substantially uniform length from a DNA substrate. Themethods generally involve contacting a DNA substrate with a Cas1polypeptide.

“Cas1” polypeptide refers to CRISPR associated (Cas) protein1. CRISPRClustered, regularly interspaced, short palindromic repeats is anacronym that describes the architecture of these repetitive elements.Cas1 (COG1518 in the Clusters of Orthologous Group of proteinsclassification system) is the best marker of the CRISPR-associatedsystems (CASS). Based on phylogenetic comparisons, seven distinctversions of the CRISPR-associated immune system have been identified(CASS1-7).

Cas1 polypeptide used in the methods described herein can be any Cas1polypeptide present in a prokaryote. In certain embodiments, a Cas1polypeptide is a Cas1 polypeptide of an archaeal microorganism. Incertain embodiments, a Cas1 polypeptide is a Cas1 polypeptide of aEuryarchaeota microorganism. In certain embodiments, a Cas1 polypeptideis a Cas1 polypeptide of a Crenarchaeota microorganism. In certainembodiments, a Cas1 polypeptide is a Cas1 polypeptide of a bacterium. Incertain embodiments, a Cas1 polypeptide is a Cas1 polypeptide of a gramnegative or gram positive bacteria. In certain embodiments, a Cas1polypeptide is a Cas1 polypeptide of Pseudomonas aeruginosa. In certainembodiments, a Cas1 polypeptide is a Cas1 polypeptide of Aquifexaeolicus. In certain embodiments, a Cas1 polypeptide is a Cas1polypeptide that is a member of one of CASS1-7. In certain embodiments,Cas1 polypeptide is a Cas1 polypeptide that is a member of CASS3. Incertain embodiments, a Cas1 polypeptide is a Cas1 polypeptide that is amember of CASS7. In certain embodiments, a Cas1 polypeptide is a Cas1polypeptide that is a member of CASS3 or CASS7.

In some embodiments, a Cas1 polypeptide is encoded by a nucleotidesequence provided in GenBank at, e.g., GeneID number: 2781520, 1006874,9001811, 947228, 3169280, 2650014, 1175302, 3993120, 4380485, 906625,3165126, 905808, 1454460, 1445886, 1485099, 4274010, 888506, 3169526,997745, 897836, or 1193018.

In certain embodiments, a Cas1 polypeptide comprises an amino acidsequence having at least about 80%, at least about 85%, at least about90%, at least about 95%, at least about 98%, at least about 99%, or100%, amino acid identity to a contiguous stretch of from about 100amino acids (aa) to about 150 aa, from about 150 aa to about 200 aa,from about 200 aa to about 250 aa, from about 250 aa to about 275 aa,from about 275 aa to about 300 aa, from about 300 aa to about 325 aa, upto the full length, of an amino acid sequence provided in FIG. 9. Incertain embodiments, Cas1 polypeptide is a Cas1 polypeptide whose aminoacid sequence is provided in FIG. 9.

In some embodiments, a Cas1 polypeptide comprises an amino acid sequencehaving at least about 80%, at least about 85%, at least about 90%, atleast about 95%, at least about 98%, at least about 99%, or 100%, aminoacid identity to a contiguous stretch of from about 100 amino acids (aa)to about 150 aa, from about 150 aa to about 200 aa, from about 200 aa toabout 250 aa, from about 250 aa to about 275 aa, from about 275 aa toabout 300 aa, from about 300 aa to about 324 aa, of the amino acidsequence depicted in FIG. 10.

In certain embodiments, Cas1 protein may be a “functional derivative” ofa naturally occurring Cas1 protein. A “functional derivative” of anative sequence polypeptide is a compound having a qualitativebiological property in common with a native sequence polypeptide.“Functional derivatives” include, but are not limited to, fragments of anative sequence and derivatives of a native sequence polypeptide and itsfragments, provided that they have a biological activity in common witha corresponding native sequence polypeptide. A biological activitycontemplated herein is the ability of the functional derivative tohydrolyze a DNA substrate into fragments. The term “derivative”encompasses both amino acid sequence variants of polypeptide, covalentmodifications, and fusions thereof. A “fusion” polypeptide is apolypeptide comprising a polypeptide or portion (e.g., one or moredomains) thereof fused or bonded to heterologous polypeptide. Examplesof fusion polypeptides include immunoadhesins which combine a portion ofthe Cas1 protein with an immunoglobulin sequence, and epitope taggedpolypeptides, which may comprise a Cas1 protein, for example, or portionthereof fused to a “tag polypeptide”. The tag polypeptide has enoughresidues to provide an epitope against which an antibody can be made,yet is short enough such that it does not interfere with nucleaseactivity of Cas1. Suitable tag polypeptides generally have at least sixamino acid residues and usually between about 6-60 amino acid residues.

“Cas1 polypeptide” encompasses a full-length Cas1 polypeptide, anenzymatically active fragment of a Cas1 polypeptide, and enzymaticallyactive derivatives of a Cas1 polypeptide or fragment thereof. Suitablederivatives of a Cas1 polypeptide or a fragment thereof include but arenot limited to mutants, fusions, covalent modifications of Cas1 proteinor a fragment thereof. Cas1 protein which includes Cas1 protein or afragment thereof, as well as derivatives of Cas1 protein or a fragmentthereof, may be obtainable from a cell or synthesized chemically or by acombination of these two procedures. The cell may be a cell thatnaturally produces Cas1 protein, or a cell that naturally produces Cas1protein and is genetically engineered to produce the endogenous Cas1protein at a higher expression level or to produce a Cas1 protein froman exogenously introduced nucleic acid, which nucleic acid encodes aCas1 that is same or different from the endogenous Cas1. In some case,the cell does not naturally produce Cas1 protein and is geneticallyengineered to produce a Cas1 protein.

Mutants of Cas1 protein may be generated by performing conservativesubstitutions which have substantially no effect on antigen binding orother antibody functions. By conservative substitutions is intendedcombinations such as those from the following groups: gly, ala; val,ile, leu; asp, glu; asn, gln; ser, thr; lys, arg; and phe, tyr. Aminoacids that are not present in the same group are “substantiallydifferent” amino acids. In certain cases, the conserved residues may notbe substituted and the substitutions limited to the non-conservedresidues.

In certain embodiments, the Cas1 protein may be purified from anorganism. The organism may be producing the Cas1 protein from anendogenous gene or from an exogenous gene. The exogenous gene may bepresent in the organism transiently or stably. For example, apolynucleotide encoding a Cas1 protein can be introduced into a suitableexpression vector. The expression vector is introduced into a suitablecell. Expression vectors generally have convenient restriction siteslocated near the promoter sequence to provide for the insertion ofpolynucleotide sequences. Transcription cassettes may be preparedcomprising a transcription initiation region, cad gene or fragmentthereof, and a transcriptional termination region. The transcriptioncassettes may be introduced into a variety of vectors, e.g. plasmid;retrovirus, e.g. lentivirus; adenovirus; and the like, where the vectorsare able to transiently or stably be maintained in the cells, usuallyfor a period of at least about one day, more usually for a period of atleast about several days to several weeks.

The various manipulations may be carried out in vitro or may beperformed in an appropriate host, e.g. E. coli. After each manipulation,the resulting construct may be cloned, the vector isolated, and the DNAscreened or sequenced to ensure the correctness of the construct. Thesequence may be screened by restriction analysis, sequencing, or thelike.

Cas1 protein may be recovered and purified from recombinant cellcultures by well-known methods including ammonium sulfate or ethanolprecipitation, acid extraction, anion or cation exchange chromatography,phosphocellulose chromatography, hydrophobic interaction chromatography,high performance liquid chromatography, affinity chromatography, proteinG affinity chromatography, for example, hydroxyapatite chromatographyand lectin chromatography, etc.

Cas1 protein may also be recovered from: products of purified cells,whether directly isolated or cultured; products of chemical syntheticprocedures; and products produced by recombinant techniques from aprokaryotic or eukaryotic host, including, for example, bacterial, yeasthigher plant, insect, and mammalian cells.

As mentioned above, methods for generating nucleic acid fragments ofsubstantially uniform length from a DNA substrate are provided. Themethods include contacting the DNA substrate with a Cas1 polypeptide.

The duration of the contacting step may be about 0.1 hour-48 hours, forexample, from about 0.1 hour to about 0.2 hour, from about 0.2 hour toabout 0.3 hour, from about 0.3 hour to about 0.5 hour, from about 0.5hour to about 1 hour, from about 0.3 hour to about 46 hours, about 0.5hour-45 hours, about 1 hour-40 hours, about 2 hours-35 hours, about 4hours-30 hours, about 6 hours-24 hours, about 8 hours -20 hours, about10 hours-18 hours, or about 12 hours-16 hours, such as, 0.3 hour, 0.5hour, 1 hour, 3 hours, 10 hours, 13 hours, 16 hours, or 18 hours.

The amount of Cas1 that is employed is one that is from about 10units/ml-50,000 units/ml, for example, from about 20 units/ml-30,000units/ml, about 30 units/ml-10,000 units/ml, about 50 units/ml-5000units/ml, about 100 units/ml-3000 units/ml, about 200 units/ml-2000units/ml, about 300 units/ml-1000 units/ml, such as, about 100 units/ml,300 units/ml, 1000 units/ml, 2000 units/ml, 5000 units/ml, 10,000units/ml, 20,000 units/ml, or 50,000 units/ml.

The temperature at which the enzymatic reaction is carried out is can befrom 4° C.-50° C., for example, about 10° C.-45° C., about 16° C.-40°C., about 20° C.-37° C., about 25° C.-35° C., about 30° C.-33° C., e.g.,10° C., 18° C., 25° C., 30° C., 37° C., or 45° C.

The contacting step may be carried out in conditions suitable for Cas1endonuclease activity. In certain embodiments, the conditions suitablefor Cas1 endonuclease activity are conditions in which a divalent metalion such as magnesium (Mg²⁺) is present. In these embodiments, the Mg²⁺concentration may range from about 1 mM-25 mM, for example, about 1.5mM-20 mM, about 2 mM-15 mM, about 2 mM-10 mM, about 3 mM-8 mM, or about5 mM-6 mM, such as, 2 mM, 2.5 mM, 3 mM, or 5 mM.

In certain embodiments, the conditions suitable for Cas1 endonucleaseactivity are conditions in which a divalent metal ion such as Manganese(Mn²⁺) is present. In these embodiments, the Mn²⁺ concentration mayrange from about 1 mM-25 mM, for example, about 1.5 mM-20 mM, about 2mM-15 mM, about 2 mM-10 mM, about 3 mM-8 mM, or about 5 mM-6 mM, suchas, 2 mM, 2.5 mM, 3 mM, or 5 mM.

Under the conditions suitable for Cas1 endonuclease activity, the pHtypically ranges from about pH 4.5-pH 10, for example, pH 5-pH 8.5, pH7-pH 8.5, or pH 7-pH 8, such as, pH 7, pH 7.5, pH 8, or pH 8.5.

The DNA substrate may be in the form of genomic DNA, linear DNA,circular DNA, double or single stranded DNA, or a mixture of two or moreof these forms of DNA. The DNA substrate may be from any organism, forexample, viruses, prokaryotes, e.g. bacteria, archaea and cyanobacteria;and eukaryotes, e.g., members of the kingdom protista, such asflagellates, amoebas and the like, amoeboid parasites, ciliates and thelike; members of the kingdom fungi, such as slime molds, acellular slimemolds, cellular slime molds, water molds, true molds, conjugating fungi,sac fungi, club fungi, imperfect fungi and the like; plants, such asalgae, mosses, liverworts, hornworts, club mosses, horsetails, ferns,gymnosperms and flowering plants, both monocots and dicots; and animals,including sponges, members of the phylum cnidaria, e.g. jelly fish,corals and the like, combjellies, worms, rotifers, roundworms, annelids,molluscs, arthropods, echinoderms, acorn worms, and vertebrates,including reptiles, fishes, birds, snakes, and mammals, e.g. rodents,primates, including humans, and the like. DNA substrates may be obtainedfrom biological fluids, e.g., blood; tissue samples; or cells (includingcell lines, cell cultures, etc.), for example. The DNA substrate may beused directly from its naturally occurring source and/or preprocessed ina number of different ways, as is known in the art.

The DNA substrate can be present in a living cell, or can be isolatedfrom a living cell. For example, the DNA substrate can be present in acell lysate. In some embodiments, the DNA substrate is isolated, and canbe purified, e.g., the DNA substrate can be at least about 50% pure, atleast about 60% pure, at least about 70% pure, at least about 80% pure,at least about 85% pure, at least about 90% pure, at least about 95%pure, at least about 98% pure, at least about 99%, or greater than 99%pure, e.g., free of macromolecules other than the DNA substrate, andfree of other contaminants.

The term “substantially uniform length” when used in reference tonucleic acid fragments, is used to refer to a population of nucleic acidfragments wherein a majority of the fragments have the same lengthwithin an acceptable variation. For example, the acceptable variation inthe length of a given fragment in the population can be at most 0.1%,1%, 2%, 5%, 8%, 10%, or 20% of the average length of fragments in thepopulation. This can be a variation in length of at most about 1nucleotide, 2 nucleotides, 3 nucleotides, 4 nucleotides, 5 nucleotides,8 nucleotides, 10 nucleotides, 13 nucleotides, 16 nucleotides, 18nucleotides, 20 nucleotides, 25 nucleotides, 30 nucleotides, 35nucleotides, 40 nucleotides, 45 nucleotides, 50 nucleotides, 55nucleotides, or 60 nucleotides. The population can be composed of atleast 50%, 60%, 70%, 80%, 90%, 95%, 99% or 99.9% fragments having aparticular length.

The substantially uniform length of the nucleic acid fragments generatedby contacting a DNA substrate with Cas1 polypeptide may be about 20 basepairs (bp)-1000 bp long, or about 30 bp-750 bp long, or about 40 bp-500bp long, or about 45 bp-250 bp long, or about 50 bp-200 bp long, orabout 60 bp-150 bp long, or about 70 bp-100bp long, for example, about30 bp, or about 50 bp, or about 80 bp, or about 100 bp, or about 150 bp,or about 200 bp. About as used herein refers to the value or rangeindicated ±1 bp, or 2 bp, or 3 bp, or 4 bp, or 5 bp.

In practicing the subject methods, the order in which the variousreagents are contacted with the DNA substrate may vary. As such, incertain embodiments, the Cas1 endonuclease may be introduced into areaction mix after the introduction of any other reagents, e.g., Mn²⁺.In some embodiments, the Cas1 endonuclease may be introduced into thereaction mix before the introduction of some other reagents, e.g.,adapter oligonucleotides. The manner in which contacting is achieved mayvary, e.g., by introducing Cas1 endonuclease into the reaction mix, byintroducing an amount of DNA substrate in a Cas1 endonuclease containingreaction mix, etc.

SCREENING METHODS

Methods for identifying modulators of Cas1 endonuclease activity areprovided. The methods may comprise assaying the nuclease activity ofCas1 in the presence of a candidate agent wherein an increase ordecrease in Cas1 endonuclease activity identifies the candidate agent asa modulator of Cas1 endonuclease activity.

Candidate agents of interest for screening include biologically activeagents of numerous chemical classes, primarily organic molecules,although including in some instances, inorganic molecules,organometallic molecules, immunoglobulins, genetic sequences, etc. Alsoof interest are small organic molecules, which comprise functionalgroups necessary for structural interaction with proteins, particularlyhydrogen bonding, and typically include at least an amine, carbonyl,hydroxyl or carboxyl group, frequently at least two of the functionalchemical groups. The candidate agents often comprise cyclical carbon orheterocyclic structures and/or aromatic or polyaromatic structuressubstituted with one or more of the above functional groups. Candidateagents are also found among biomolecules, including peptides,polynucleotides, saccharides, fatty acids, steroids, purines,pyrimidines, derivatives, structural analogs or combinations thereof.

Compounds may be obtained from a wide variety of sources includinglibraries of synthetic or natural compounds. For example, numerous meansare available for random and directed synthesis of a wide variety oforganic compounds, including biomolecules, including expression ofrandomized oligonucleotides and oligopeptides. Alternatively, librariesof natural compounds in the form of bacterial, fungal, plant and animalextracts are available or readily produced. Additionally, natural orsynthetically produced libraries and compounds are readily modifiedthrough conventional chemical, physical and biochemical means, and maybe used to produce combinatorial libraries. Known pharmacological agentsmay be subjected to directed or random chemical modifications, such asacylation, alkylation, esterification, amidification, etc. to producestructural analogs.

A plurality of assays may be run in parallel with differentconcentrations to obtain a differential response to the variousconcentrations. As known in the art, determining the effectiveconcentration of an agent typically uses a range of concentrationsresulting from 1:10, or other log scale, dilutions. The concentrationsmay be further refined with a second series of dilutions, if necessary.Typically, one of these concentrations serves as a negative control,i.e. at zero concentration or below the level of detection of the agentor at or below the concentration of agent that does not give adetectable change in nuclease activity.

The assaying may comprise contacting the candidate agent to a reactionmix that includes Cas1, a source of divalent metal ion, and a DNAsubstrate; measuring the activity of Cas1 in the reaction mix, comparingthe measured activity to the activity of a control reaction mix thatincludes Cas1, a source of divalent metal ion, and a DNA substrate butnot the candidate agent being tested; and identifying a candidate agentthat increases or decreases the Cas 1 endonuclease activity.

Any type of nuclease assay may be used. In certain examples, the assaymay be plasmid DNA digestion assays, such as, supercoiled DNA digestionassay or linear DNA digestion assay, or a hyperchromicity assay.

Plasmid DNA Digestion Assays

A supercoiled plasmid DNA digestion assay measures the conversion ofsupercoiled double-stranded plasmid, e.g., pBR322 DNA to relaxed(nicked), linear, and fragmented forms. The linear DNA digestion assaymeasures the conversion of linear double-stranded DNA to degraded forms.

Cas1 protein with or without a candidate agent may be added to asolution containing supercoiled double-stranded plasmid or lineardouble-stranded DNA in an appropriate reaction mix including a buffer,bovine serum albumin (BSA), salt, divalent metal ion, etc. and incubatedat around 25° C. At various times, aliquots of the reaction mixtures maybe removed and quenched by the addition of a metal chelator, such as, 25mM EDTA (ethylene-diamine-tetra-acetic acid), together with reagents forelectrophoretic analysis of DNA, such as, xylene cyanol, bromphenolblue, and glycerol. The integrity of the supercoiled or linear DNA inthe quenched samples may be analyzed by electrophoresis of the sampleson agarose gels (for example, 0.8% weight/vol.). After electrophoresis,the gels may be stained with a solution of ethidium bromide and the DNAin the gels visualized by ultraviolet light. The relative amounts ofsupercoiled, relaxed, and linear forms of plasmid DNA may be determinedby scanning of the gels with a FluorImager and quantitating the amountof DNA in the bands of the gel that corresponded to those differentforms.

In the supercoiled DNA digestion assay, the overall activity of the Cas1may be measured as the initial rate of disappearance of supercoiled DNA(as a result of it being converted to relaxed (nicked), linear, ordegraded DNA), normalized relative to the rate observed with Cas1without candidate agent. The ratio of linearized to relaxed forms of DNAmay also be determined relative to that observed with Cas1 withoutcandidate agent. In the linear DNA digestion assay, the activity of Cas1with candidate agent may be measured as the initial rate ofdisappearance of linear DNA (as a result of it being converted todegraded forms), normalized relative to the rate observed with Cas1without candidate agent.

Modulators of Cas1 endonuclease activity that increase Cas1 activity maybe used in vitro or in vivo to enhance Cas1 activity. For instance, suchmodulators may be added to compositions of Cas1 or used in cell culturesin a laboratory setting. For example, such modulators may serve toenhance the activity of an endogenous Cas1 expressed by a cell in a cellculture and provide an enhanced protection to infection by phages andother pathogens.

Modulators of Cas1 endonuclease activity that decrease Cas1 activity maybe used in vitro or in vivo to decrease Cas1 activity. For instance,such modulators may be used to increase the susceptibility of anorganism that utilizes Cas1 to defend against viral or other pathogensto such pathogens. Therefore, Cas1 modulators that decrease Cas1activity may be used to weaken an organism, for example.

UTILITY Nucleic Acid Analysis

Cas1 may be used to generate DNA fragments for use in a variety ofresearch and diagnostic methods. For example, the nucleic acid fragmentsof substantially uniform length generated by using Cas1 may be used forsequencing, genotyping, copy number variation analysis, DNA methylationanalysis, and the like.

In some embodiments, the nucleic acid fragments of substantially uniformsize generated by using Cas1 do not usually require size selection by asize separation method such as gel purification and as such almost allof the nucleic acid fragments are available for subsequent use. This isespecially advantageous in analysis of nucleic acid from samples wherethe amount of material is limited, such as biopsies, laser capturedcells, limited archival tissues, embryoid bodies, small model systems,and difficult to cultivate organisms such as Microsporidia.

Nucleic Acid Fragment Libraries

The nucleic acid fragments of substantially uniform size range generatedby using Cas1 may include fragments with blunt ends and/or 3′ and 5′overhanging ends. The fragment ends may be repaired using methods orkits known in the art to generate ends that are convenient, for example,for insertion into blunt sites in cloning vectors or for ligation ofadapters onto the ends of each fragment.

Nucleic acid fragment libraries may be prepared from the nucleic acidfragments. Following end repair, double stranded adaptor polynucleotidesequences may be ligated to both ends of the nucleic acid fragments toform adaptor-fragment-adaptor polynucleotide sequences.

Ligation methods are known in the art and utilize standard methods(Sambrook and Russell, Molecular Cloning, A Laboratory Manual, thirdedition Cold Spring Harbor Laboratory Press (2001)). Such methodsutilize ligase enzymes such as DNA ligase to effect or catalyze joiningof the ends of the two polynucleotide strands of, in this case, theadaptor duplex construct and the nucleic acid fragment, such thatcovalent linkages are formed.

The adaptor constructs may also contain a region on one, or both, of thestrands that does not hybridize with a sequence on the other strand ofthe adaptor. Such “mismatched” adaptors can serve as priming sites foramplification reactions. Optionally, the adaptor-fragment-adaptormolecules may be purified from any components of the ligation reaction,such as enzymes, buffers, salts and the like. Suitable purificationmethods are known in the art and utilize standard methods (Sambrook andRussell, Supra).

In further embodiments, the adaptor-fragment-adaptor molecules may beamplified. The contents of an amplification reaction are known by oneskilled in the art and include appropriate reagents (such as,deoxyribonucleotide triphosphates (dNTPs)), enzymes (e.g. a DNApolymerase) and buffer components required for an amplificationreaction. Generally amplification reactions use at least twoamplification primers, often denoted ‘forward’ and ‘reverse’ primers(primer oligonucleotides) that are capable of annealing specifically toa part of the polynucleotide sequence to be amplified under conditionsencountered in the primer annealing step of each cycle of anamplification reaction. In certain embodiments the forward and reverseprimers may be identical.

The nucleic acid fragment libraries comprising cloned nucleic acidfragments or nucleic acid fragment to which adapters have been ligatedmay be used in research or diagnostic methods.

Generating Labeled Probes

The nucleic acid fragments generated by using Cas1 may be labeled togenerate labeled nucleic acid fragments that can be used a probes, e.g.,for use in research and/or diagnostic methods.

Any label detectable by spectroscopic, photochemical, biochemical,immunochemical, electrical, optical or chemical means may be used tolabel the nucleic acid fragments. Useful labels include biotin forstaining with labeled streptavidin conjugate, magnetic beads (e.g.,Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine,green fluorescent protein, cyanins and the like), radiolabels (e.g., ³H,³⁵S, ¹⁴C, or ³²P, enzymes (e.g., horseradish peroxidase, alkalinephosphatase and others commonly used in enzyme-linked immunosorbentassay), and colorimetric labels such as colloidal gold or colored glassor plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.Patents teaching the use of such labels include U.S. Pat. Nos.3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and4,366,241, which are herein incorporated by reference.

The labels may be incorporated into the nucleic acid fragments by any ofa number of means well known to those of skill in the art. The label maybe simultaneously incorporated during the amplification step. Thus, forexample, polymerase chain reaction (PCR) with labeled primers or labelednucleotides will provide a labeled amplification product. In certainembodiment, a label may be added directly to the nucleic acid fragmentsor to the amplification product after the amplification is completed.Means of attaching labels to nucleic acids are well known to those ofskill in the art and include, for example nick translation orend-labeling, by kinasing of the nucleic acid and subsequent attachmentof a nucleic acid linker joining the nucleic acid to a label. Standardmethods may be used for labeling a polynucleotide fragment, for example,as set out in Maniatis et al., Molecular Cloning, A Laboratory Manual,Cold Spring Harbor Publication (1982).

Sequencing

Any suitable method of sequencing may be used to determine a sequenceread of the nucleic acid fragments prepared using Cas1. Suitable methodsof sequencing include the use of sequencing by addition of nucleotidebases, for example sequencing by synthesis (SBS) using nucleosidetriphosphates and DNA polymerases (as described in US 2007/0166705 andUS 2006/0240439 respectively), or using oligonucleotide cassettes andligases (as described in U.S. Pat. No. 6,306,597, US 2008/0003571 orScience, 309:5741, 1728-1732 (2005)).

In “sequencing by synthesis” or SBS a new polynucleotide strandbase-paired to a template strand is built up in the 5′ to 3′ directionby successive incorporation of individual nucleotides complementary tothe template strand. In one embodiment of SBS the different nucleotidetriphosphates used in the sequencing reaction are each labeled withdifferent labels permitting determination of the identity of theincorporated nucleotide as successive nucleotides are added. The labelednucleotide triphosphates also have a 3′ blocking group which preventsfurther incorporation of complementary bases by the polymerase. Thelabel of the incorporated base can then be determined and the blockinggroup removed to allow further polymerization to occur. Labelednucleotides are described in WO07135368.

Sequencing multiple nucleic acid fragments produced by Cas1 may beperformed in parallel using arrays, wherein multiple polynucleotidefragments (with or without adapters) are immobilized on an array and aresequenced in parallel. For example, nucleotide(s) is(are) incorporatedinto a strand of nucleic acid complementary to the template nucleic andeach nucleotide is fluorescently labeled. The inclusion of a fluorescentlabel facilitates detection/identification of the base present in theincorporated nucleotide(s). Appropriate fluorophores are well known inthe art. Use of the polynucleotide fragments of substantially uniformsize in nucleic acid analysis is described in US Application PublicationNo. 20090191563, which is herein incorporated by reference.

Treatment Methods Biofilms

Cas1 polypeptide may be used to reduce or inhibit biofilms.

Biofilms form on living and non-living surfaces and represent aprevalent mode of microbial life in natural, industrial and hospitalsettings. Biofilms have been found to be involved in a wide variety ofmicrobial infections in the body, by one estimate 80% of all infections.Infectious processes in which biofilms have been implicated includecommon problems such as urinary tract infections, catheter infections,middle-ear infections, formation of dental plaque, gingivitis, and lesscommon but more lethal processes such as endocarditis, infections incystic fibrosis, and infections of permanent indwelling devices such asjoint prostheses and heart valves. More recently it has been noted thatbacterial biofilms may impair cutaneous wound healing and reduce topicalantibacterial agents' efficiency in healing or treating infected skinwounds. Biofilms can also form on the inert surfaces of implanteddevices such as catheters, prosthetic cardiac valves and intrauterinedevices.

Cas1 protein may be employed to prevent microorganisms from adhering tosurfaces or growing on surfaces, which surfaces may be porous, soft,hard, semi-soft, semi-hard, regenerating, or non-regenerating. Thesesurfaces include, but are not limited to, polyurethane, metal, alloy, orpolymeric surfaces in medical devices, enamel of teeth, and cellularmembranes in animals, preferably, mammals, more preferably, humans. Thesurfaces may be coated or impregnated with the Cas1 protein prior touse. Alternatively, the surfaces may be treated with Cas1 protein tocontrol, reduce, or eradicate the microorganisms adhering to thesesurfaces.

Cas1 may be used to reduce the viscoelasticity of DNA-containingmaterial, including sputum, mucus, or other pulmonary secretions ofpatients with pulmonary disease. Abnormal viscous or inspissatedsecretions (e.g., sputum, mucus, or other pulmonary secretions) arecommon in pulmonary diseases such as acute or chronic bronchialpneumonia, including infectious pneumonia, bronchitis ortracheobronchitis, bronchiectasis, cystic fibrosis, asthma,tuberculosis, and fungal infections. For such therapies, a solution orfinely divided dry preparation of Cas1 may be instilled in conventionalfashion into the airways (e.g., bronchi) or lungs of a patient, forexample by aerosolization.

Cas1 polypeptide can also useful for treatment of abscesses or severeclosed-space infections in conditions such as emphysema, meningitis,abscess, peritonitis, sinusitis, periodontitis, pericarditis,pancreatitis, cholelithiasis, endocarditis and septic arthritis, as wellas in topical treatments in a variety of inflammatory and infectedlesions such as infected lesions of the skin and/or mucosal membranes,surgical wounds, ulcerative lesions and burns. Cas1 may improve theefficacy of antibiotics used in the treatment of such infections (e.g.,gentamicin activity is markedly reduced by reversible binding to intactDNA).

Cas1 protein may contribute to the treatment of cystic fibrosis. Incystic fibrosis, Pseudomonas aeruginosa reside on the lungs of cysticfibrosis patients. Cas1 protein may prevent, reduce, or eradicate thebiofilm of Pseudomonas aeruginosa.

Cas1 polypeptide can be used as a preprocedural rinse for surgery, as anantiseptic rinse, a topical antiseptic and a catheter lock solution.

Cas1 polypeptide may also be used for enhancing efficacy of antibiotictherapy against bacterial infections by administration of apharmaceutical composition of Cas1 polypeptide in combination with orprior to administration of an antibiotic.

Cas1 protein or active fragment or derivative thereof can beincorporated in a liquid disinfecting solution. Such solutions mayfurther comprise antimicrobials or antifungals such as alcohol,providone-iodine solution and antibiotics as well as preservatives.These solutions can be used, for example, as disinfectants of the skinor surrounding area prior to insertion or implantation of a device suchas a catheter, as catheter lock and/or flush solutions, and asantiseptic rinses for any medical device including, but not limited tocatheter components such as needles, Leur-Lok connectors, needlelessconnectors and hubs as well as other implantable devices. Thesesolutions can also be used to coat or disinfect surgical instrumentsincluding, but not limited to, clamps, forceps, scissors, skin hooks,tubing, needles, retractors, scalers, drills, chisels, rasps and saws.

Cas1 protein may be formulated into a variety of formulations fortherapeutic administration. More particularly, Cas1 protein as disclosedherein can be formulated into pharmaceutical compositions by combinationwith appropriate pharmaceutically acceptable carriers or diluents, andmay be formulated into preparations in solid, semi-solid, liquid forms,such as, powders, granules, solutions, injections, inhalants, gels,hydrogels, microspheres, etc. Pharmaceutical compositions can include,depending on the formulation desired, pharmaceutically-acceptable,non-toxic carriers of diluents, which are defined as vehicles commonlyused to formulate pharmaceutical compositions for animal or humanadministration. The diluent is selected so as not to affect thebiological activity of the combination. Examples of such diluents aredistilled water, buffered water, physiological saline, phosphatebuffered saline (PBS), Ringer's solution, dextrose solution, and Hank'ssolution. In addition, the pharmaceutical composition or formulation caninclude other carriers, adjuvants, or non-toxic, nontherapeutic,nonimmunogenic stabilizers, excipients and the like. The compositionscan also include additional substances to approximate physiologicalconditions, such as pH adjusting and buffering agents, toxicityadjusting agents, wetting agents and detergents.

A pharmaceutical composition comprising Cas1 polypeptide may be an oralpreparation, an injection or an aerosol preparation. Preparationssuitable for oral administration may be a liquid obtained by dissolvingan effective amount of Cas 1 in diluents such as water, physiologicalsaline, a capsule, a sachet or a tablet containing an effective amountof Cas1, suspension containing an effective amount of Cas1 suspended inan appropriate dispersion medium, and emulsion prepared by suspending asolution containing an effective amount of Cas1 dissolved in anappropriate dispersion medium and emulsifying the suspension. Theaerosol preparation may include Cas1 compressed withdichlorodifluoromethane, propane or nitrogen or a non-compressedpreparation such as nebulizer and atomizer, and can be administered byinhalation or spraying into airways and the like.

A Cas1 pharmaceutical composition may be combined with or administeredin concert with one or more other pharmacologic agents, such asantibiotics, bronchodilators, anti-inflammatory agents, mucolytics (e.g.n-acetyl-cysteine), actin binding or actin severing proteins (e.g.,gelsolin; Matsudaira et al., Cell 54:139-140 (1988); Stossel, et al.,PCT Patent Publication No. WO 94/22465 (published Oct. 13, 1994)),protease inhibitors, gene therapy product (e.g., comprising the cysticfibrosis transmembrane conductance regulator (CFTR) gene, Riordan, etal., Science 245:1066-1073 (1989)), glucocorticoids, or cytotoxicagents.

The pharmaceutical composition can also include any of a variety ofstabilizing agents, such as an antioxidant for example. The Cas1polypeptide of a composition can also be complexed with molecules thatenhance its in vivo attributes. Such molecules include, for example,carbohydrates, polyamines, amino acids, other peptides, ions (e.g.,sodium, potassium, calcium, magnesium, manganese), and lipids. Cas1 maybe incorporated into liposomes or microvesicles.

Wound dressings including but not limited to sponges or gauzes can beimpregnated with a composition comprising Cas1 polypeptide or activefragment or derivative thereof to prevent or inhibit bacterial or fungalattachment and reduce the risk of wound infections. Similarly, cathetershields as well as other materials used to cover a catheter insertionsites can be coated or impregnated with Cas1 polypeptide or activefragment or derivative thereof to inhibit bacterial or fungal biofilmattachment thereto. Adhesive drapes used to prevent wound infectionduring high risk surgeries can be impregnated with the isolated proteinor active fragment or variant thereof as well. Additional medicaldevices which can be coated with Cas1 polypeptide or active fragment orderivative thereof include, but are not limited, central venouscatheters, intravascular catheters, urinary catheters, Hickmancatheters, peritoneal dialysis catheters, endotracheal catheters,mechanical heart valves, cardiac pacemakers, arteriovenous shunts,scleral buckles, prosthetic joints, tympanostomy tubes, tracheostomytubes, voice prosthetics, penile prosthetics, artificial urinarysphincters, synthetic pubovaginal slings, surgical sutures, boneanchors, bone screws, intraocular lenses, contact lenses, intrauterinedevices, aortofemoral grafts and vascular grafts. Exemplary solutionsfor impregnating gauzes or sponges, catheter shields and adhesive drapesor coating catheter shields and other medical devices include, but arenot limited to, PBS (pH approximately 7.5) and bicarbonate buffer (pHapproximately 9.0).

The pharmaceutical compositions can be administered for prophylacticand/or therapeutic treatments. Toxicity and therapeutic efficacy of aCas1 polypeptide can be determined according to standard pharmaceuticalprocedures in cell cultures and/or experimental animals, including, forexample, determining the LD₅₀ (the dose lethal to 50% of the population)and the ED₅₀ (the dose therapeutically effective in 50% of thepopulation). The dose ratio between toxic and therapeutic effects is thetherapeutic index and it can be expressed as the ratio LD₅₀/ED₅₀.

The data obtained from cell culture and/or animal studies can be used informulating a range of dosages for humans. The dosage of an activeingredient typically lines within a range of circulating concentrationsthat include the ED₅₀ with low toxicity. The dosage can vary within thisrange depending upon the dosage form employed and the route ofadministration utilized.

The components used to formulate the pharmaceutical compositions arepreferably of high purity and are substantially free of potentiallyharmful contaminants (e.g., at least National Food (NF) grade, generallyat least analytical grade, and more typically at least pharmaceuticalgrade). Moreover, compositions intended for in vivo use are usuallysterile.

The pharmaceutical compositions may be administered using any medicallyappropriate routes, e.g., an epithelial route such as intranasal,pulmonary, sublingual, oral, buccal, or other routes such asintravascular (intravenous, intraarterial, intracapillary), injectioninto the cerebrospinal fluid, intracavity or direct injection into atissue.

The effective amount of a therapeutic composition to be given to aparticular patient will depend on a variety of factors, several of whichwill be different from patient to patient. Utilizing ordinary skill, thecompetent clinician will be able to optimize the dosage of a particulartherapeutic in the course of routine clinical trials.

KITS

Also provided herein are kits that include one or more containers of thecomponents of the compositions described herein.

A subject kit includes at least an isolated Cas1 polypeptide. In someembodiments, the Cas1 polypeptide is lyophilized. In some embodiments,the containers may include a lyophilized Cas1 polypeptide. In someembodiments, the containers may include Cas1 polypeptide suspended in anaqueous medium, where the aqueous medium may be a buffer, for example,PBS, Tris-buffered saline, Tris-Hydrochloride. The medium may includeaddition components, such as glycerol, or other agents, for example,BSA, dithiothreitol (DTT), that stabilize proteins. The medium mayfurther comprise salt (e.g., sodium chloride, or potassium chloride),additives to prevent microbial growth, such as EDTA, EGTA (ethyleneglycol tetra-acetic acid). The kit may further include a container ofreaction buffer which may be used in a reaction mixture comprising Cas1polypeptide. The reaction buffer may include a divalent metal ion, forexample, Mg²⁺ or Mn²⁺. In addition the reaction buffer may include oneor more of: a buffer, one or more salts, glycerol, DTT, BSA, etc. Othersuitable components include, e.g., a nuclease inhibitor, a proteaseinhibitor, and the like.

In some cases, the kit may include a first container comprising a Cas1polypeptide; and a second container comprising at least a secondcomponent, e.g., a solution comprising a divalent metal ion, forexample, Mg²⁺ or Mn²⁺; a protease inhibitor; a nuclease inhibitor; etc.In some case, the kit may include a first container comprising a Cas1polypeptide and a divalent metal ion, for example, Mg²⁺ or Mn²⁺. In somecase, the kit may include a first container comprising a Cas1polypeptide and a divalent metal ion, for example, Mg²⁺ or Mn²⁺; and asecond container comprising a reaction buffer.

The kits may further include a suitable set of instructions, generallywritten instructions, relating to the use of a Cas1 polypeptide forhydrolyzing a DNA substrate in vitro or in vivo.

EXAMPLES

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the present invention, and are not intended to limit thescope of what the inventors regard as their invention nor are theyintended to represent that the experiments below are all or the onlyexperiments performed. Efforts have been made to ensure accuracy withrespect to numbers used (e.g. amounts, temperature, etc.) but someexperimental errors and deviations should be accounted for. Unlessindicated otherwise, parts are parts by weight, molecular weight isweight average molecular weight, temperature is in degrees Celsius, andpressure is at or near atmospheric. Standard abbreviations may be used,e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec,second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb,kilobase(s); bp, base pair(s); nt, nucleotide(s); and the like.

Materials and Methods

PA14_Cas1 expression and purification. Genomic DNA isolated from strain14 of P. aeruginosa (PA14) was used as the template for PCRamplification of the cas1 gene (PA14_33350; GeneID: 4380485) (Lee etal., 2006). The PCR product generated from PA14Cas1_FWDcaccatggacgacatttctcccag (SEQ ID NO:23) and PA14Cas1_REVttatcatgcggatactgtgctc (SEQ ID NO:24) was cloned into pENTR™/TEV/D-TOPOusing the Gateway system (Invitrogen). The cas1 sequence was confirmedby DNA sequencing and then recombined into a Gateway compatibleexpression vector (pHMGWA) containing an N-terminal His6MBP tag. TheHis6MBP-Cas1 fusion protein was expressed in BL21(DE3) cells that wereinduced with 0.5 mM isopropyl-β-D-thiogalactopyranoside (IPTG) atOD₆₀₀=0.5 in overnight cultures grown at 16° C. Cells from the overnightexpression cultures were harvested by centrifugation (10,000×g) for 20minutes. The cell pellet was resuspended in lysis buffer (20 mMimidazole, 0.01% Triton X-100, 100 u/ml DNaseI, 2 mMTris(2-carboxyethyl) phosphine hydrochloride (TCEP), 0.5 mMphenylmethylsulfonyl fluoride (PMSF), protease inhibitors, 10% glycerol)and the slurry was sonicated on ice for 2 min in 10 second bursts. Thelysate was clarified by centrifugation (22,000×g for 20 min) and theHis6MBP-Cas1 fusion protein was bound to Ni-NTA affinity resin in batch(Qiagen). His6MBP-Cas1 was eluted from the resin in 50 ml lysis buffercontaining 300 mM imidazole. The eluted protein was dialyzed at 4° C.overnight against gel filtration buffer (20 mM HEPES pH 7.5, 500 mM KCl,1 mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP), 5% Glycerol) inthe presence of tobacco etch virus (TEV) protease to remove theN-terminal His6MBP tag. The protein was concentrated (Amicon) forfurther purification on tandem Superdex 75 (16/60) sizing columns. Asimilar strategy was used for the expression and purification of theselenomethionine-containing protein, with the only major exception beingthe expression media. Briefly, Escherichia coli BL21(DE3) transformedwith the Cas1 expression construct (PaCas1/pHMGWA) were grown in M9minimal media supplemented with ampicillin. At an OD₆₀₀ of 0.5, thefollowing amino acids were added to inhibit methionine biogenesis and toallow for selenomethionine incorporation (Leu, Ile, Val: 50 mg/L; Phe,Lys, Thr: 100 mg/L; Selenomethionine: 75 mg/L) (Vanduyne et al., 1993).IPTG (0.5 mM) was added 15 minutes later and the culture was maintainedat 16° C. overnight. The purified protein was concentrated to 9 mg/ml in20 mM HEPES pH 7.5, with 100 mM KCl, 1 mM TCEP and 5% Glycerol.

Crystallization, data collection and structure determination. Nativecrystals were grown at 18° C. by vapor diffusion in hanging dropscomposed of equal volumes of protein solution (16 mg/ml Cas1 in 20 mMHEPES pH 7.6, 100 mM KCl, 1 mM TECP, 5% glycerol) and reservoir solution(250 mM CaCl2, 50 mM HEPES pH 7.6, 10% PEG8000). OptimizedSeMet-containing crystals were grown at 18° C. by vapor diffusion inhanging drops composed of equal volumes of protein solution (12 mg/mlCas1 in 20 mM HEPES pH 7.6, 100 mM KCL, 1 mM TECP, 5% glycerol) andreservoir solution (250 mM calcium acetate, 50 mM HEPES pH7.8, 6%PEG5000 MME). All crystals were cryo-protected by soaking in wellsolution supplemented with 30% glycerol for 15 seconds and then flashcooled in liquid nitrogen.

Diffraction data were collected at the Advanced Light Source (beamline8.2.2), Lawrence Berkeley National Laboratory. Phases for the Cas1structure were determined from a highly redundant single wavelengthanomalous dispersion (SAD) data set collected at the Au L-III edge(λ=1.036652 Å) using native crystals soaked in 10 mM KAu(CN)2 for 10minutes. Data with an I/sigma of greater than 2.0 was measured out to3.0 Å resolution. Data were processed in space group P212121 using XDS(Kabsch, 1988; Kabsch, 1993). SOLVE (Terwilliger and Berendzen, 1999)was used to locate six gold atoms in the crystallographic asymmetricunit and to calculate initial phases.

Density modification and initial model building was performed usingRESOLVE (Adams et al., 2002). A crude initial model was constructed bymanually placing alpha helices using COOT (Emsley and Cowtan, 2004). Themodel was extended by automated model building using RESOLVE (Adams etal., 2002; Terwilliger, 2000, 2003) and Buccaneer (Cowtan, 2006) andcompleted by iterative rounds refinement and model building using Phenixrefine (Afonine et al., 2005) and COOT (Emsley and Cowtan, 2004),respectively. The final model was refined against an isomorphous 2.17 Ådata set measured from selenomethionine-containing crystals, yielding aR_(cryst) of 20.3% and R_(free) of 25.8%.

To locate the metal binding site in Cas1, SeMet-containing Cas1 crystals(grown from 250 mM calcium chloride, 50 mM HEPES pH 7.8, 12% PEG5000MME) were soaked in 5 mM MnCl₂ for two hours. Diffraction data wasmeasured at the K absorption edge (1.8842 Å). Manganese ions wereincluded in the refinement using elbow (http followed by ://www.followed by phenix-online.org/ followed by documentation/ followed byelbow. followed by htm).

Activity assays. Purified recombinant Cas1 from PA14 (15.3 μM) wasincubated at 25° C. with 1 μg of the indicated nucleic acid substrate(0.05 μM dsDNA, 0.05 μM ssDNA, 0.3 μM dsRNA and 0.6 μM ssRNA) in thepresence of 20 mM HEPES pH 7.5 and 100 mM KCl at 25° C. for 90 minutes.Each reaction was supplemented with no metal (NM) or with 2.5 mMmagnesium (Mg²⁺), manganese (Mn²⁺), cobalt (Co²⁺), calcium (Ca²⁺), iron(Fe³⁺), zinc (Zn²⁺), or EDTA, as indicated. RNA substrates weregenerated by in vitro transcription of the first 10 repeats and ninespacers of CRISPR2 cloned into the plasmid vector pUC19. In vitrotranscripts from both strands of CRISPR2 were generated using T7 RNApolymerase at 37° C. for 2-5 hrs, in a reaction including: 30 mM Tris pH8.4, 25 mM MgCl₂, 5 mM of each nucleotide tri-phosphate, 10 mM TritionX-100, 10 mM dithiothreitol (DTT), 2 mM spermidine, 200 nM linearizeddsDNA template (CRISPR2-pUC19). Transcripts were purified on denaturingpolyacrylamide gels. Double-stranded CRISPR2 RNA substrates weregenerated by annealing the forward and reverse transcripts at 65° C. for10 minutes. All nuclease assays were performed at 25° C.

ACCESSION NUMBERS. Refined models and experimental structure factors forthe Cas1 protein from P. aeruginosa (PaCas1) have been deposited in theProtein Data Bank under accession number 3GOD.

Example 1 Identification of the P. aeruginosa PA14 cas1 Gene

P. aeruginosa, a gram-negative bacterium, is an opportunistic humanpathogen known for its ability to grow in low-oxygen environmentsincluding the tissues of immunocompromised or cystic fibrosis patients.To investigate the function of the Cas1 protein, CRISPR elements in thegenome of Pseudomonas aeruginosa, strain 14 (PA14) (Lee et al., 2006)were focused upon. Using a CRISPR-finding algorithm, two repetitivegenetic elements with the distinct repeat-spacer-repeat architecturecharacteristic of CRISPRs have been identified in the PA14 genome(Grissa et al., 2007). These two elements flank a cassette of six openreading frames (ORFs) that are annotated as hypothetical proteins. Blastanalysis (basic local alignment search tool) identified each of theseORFs (PA14_33300-33350) as CRISPR-associated (cas) genes (Altschul etal., 1997; Zegans et al., 2008).

Based on phylogenetic comparisons, seven distinct versions of theCRISPR-associated immune system have been identified (CASS1-7) (Makarovaet al., 2006). The identity and genomic arrangement of the PA14 casgenes are characteristic of CASS3. Blast analysis of the predictedprotein sequence for PA14 cas gene 33350 identified homologous sequencesmost typically annotated as Cas1 (COG1518). Cas1, a ˜36 kD protein, hasno obvious homology to proteins of known function. Due to itsconservation across CRISPR systems, a molecular structure and functionfor the Cas1 protein from PA14 was determined.

Example 2 Crystal Structure of Cas1 Revealed a Novel Fold

The cas1 gene from P. aeruginosa was cloned and over-expressed in E.coli. The purified protein was crystallized by vapor diffusion inhanging drops with a PEG-salt precipitant. The Cas1 structure was solvedby SAD (single-wavelength anomalous dispersion) using a gold derivativeand the final structure was refined against a 2.17 Å data set, yieldingan R_(cryst) of 20.3% and an R_(free) of 25.8%.

The Cas1 protein has a novel three-dimensional fold consisting of twostructurally distinct domains (FIG. 1). The N-terminal β-strand domainincludes residues 1-106 and is composed of 10 β-strands and twoα-helices (yellow). This β-strand domain is connected to a C-terminalα-helical domain by a flexible linker (residues 107-112, green). Theα-helical domain, including residues 113-324, comprises 10 α-helices(gray). Conserved residues are colored red. Side chains of the fouruniversally conserved residues (E190, N223, H254, and D265), as well astrongly conserved aspartic acid at position 268 (D or E) are displayedas sticks were oxygen's are red, nitrogen's are blue and carbons aregray. Residues E190, H254 and D268 coordinate a manganese ion (greensphere). All ribbon diagrams were prepared using PYMOL (DeLano, 2002).

Comparison of the four Cas1 molecules (A-D) in the asymmetric unit ofthe crystal shows that their α-helical domains are nearly identical withan average root mean square deviation (r.m.s.d.) for equivalentlypositioned Cα atoms between residues 113-324 of 0.32 Å. There are,however, substantial differences in the fold and orientation of theβ-strand domains (FIG. 2). Thus, the linker connecting the α and βdomains serves as a hinge that allows the two domains of a singlemolecule to be positioned in different relative orientations (FIG. 2Panels A and B). FIG. 2, Panel shows that the C-terminal α-helicaldomains of molecules A and C superimpose (residues 113-321) with anaverage r.m.s.d of 0.40 Å. The β-strand domains of these two moleculesare in different orientations (two-way arrow) with respect to theirα-helical domains. Coloring of molecule A is consistent with that inFIG. 1. Molecule C is colored light blue, with conserved residuescolored pink. The α-helical and β-strand domains of molecules A and Bare in the same relative orientation and the two molecules superimposewith an average r.m.s.d. of 0.20 Å for 318 equivalent Cα positionsbetween residues 4-321. Molecules C and D are similar to one-another(0.57 Å Cα r.m.s.d.), but distinct from A and B. FIG. 2, Panel B shows aview down the barrel of α8 after rotation of 90° about the Y-axis and20° about the X-axis. Pronounced structural differences occur at theN-terminus and in the positions of β-strands 8 and 9 (FIG. 2, Panel C).Molecules A and B have a well-ordered N-terminal α-helix (residues6-16), whereas this region is disordered in molecule C. The N-terminusof molecule D forms an extended coil that is oriented in the oppositedirection from that observed in molecules A and B; this coil formscrystal contacts with β-strands 3 and 4 (residues 36-52) in molecule C.In FIG. 2, panel C the superimposed β-strand domains are rotated 90°about the X-axis and viewed from the perspective of the α-helicaldomain. β-strands 8 and 9 form a short anti-parallel β-sheet in moleculeA. This feature is not observed in molecule C, instead the sequence thatwould be part of β-strand 9 forms part of the unordered linker.Glutamate 96 (teal sticks) relates the primary sequence of bothmolecules to secondary structure elements in this region.

Cas1 molecules with different β-strand domain structures form dimers inthe asymmetric unit of the crystal, yielding A-C and B-D homodimers. TheCas1 homodimer is shaped like a butterfly, where the α-helical andβ-strand domains of each molecule represent the upper and lower lobe ofeach ‘wing’ (FIG. 3). The wingspan of the Cas1 homodimer is −86 Å, andeach wing stands ˜60 Å from top to bottom and ˜46 Å thick. The twomolecules in each dimer are related by a pseudo-two-fold axis ofsymmetry centered about the dimer interface. Extensive hydrogen bondingand two salt bridges (C/Glu96-A/His248; C/Asp98-A/Arg259) at the dimerinterface result in 1,761 Å2 of buried surface area. Notably, the dimeris maintained in high salt (500 mM) buffers and elutes from a calibratedSuperdex S-75 size exclusion column with a retention volume consistentwith a protein of ˜84 kDa, suggesting that Cas1 (˜36 kDa) is homodimericin solution. FIG. 3, Panel A shows conserved residues colored red inmolecule A and pink in molecule C, side chains of the four universallyconserved residues displayed as sticks, two of the four universallyconserved residues (Glu190 and His254) and a well conserved asparticacid at position 268 (Asp or Glu) coordinate a manganese ion (greensphere). FIG. 3, Panel B provides a look down the dimer interface aftersixty-degree rotation about the Y-axis.

Structural comparisons performed using the DALI (Holm and Sander, 1993)and VAST (Gibrat et al., 1996) servers reveal a structural homolog ofthe Cas1 protein. The Cas1 structure from P. aeruginosa (PaCas1) is mostsimilar (Z-score 17.5) to the unpublished structure of a hypotheticalprotein from Aquifex aeolicus (pdb id:2YZS). The amino acid sequences ofthese two proteins are highly divergent (17.6% identity, 37.0%similarity) and are not recognized as homologs by BlastP (Altschul etal., 1997). However, further examination of the A. aeolicus protein(gene ID: 1193018) using PSI-Blast and genomic neighborhood analysisreveals that this is a Cas1 protein flanked by cas genes that are mostsimilar to those of the CASS7 subtype.

The Cas1 protein from A. aeolicus (AaCas1) shares a similar tertiary andquaternary architecture to the Cas1 protein structure from P. aeruginosa(FIG. 4, Panel A; FIG. 8). FIG. 4, Panel A shows that the α-helicaldomains of molecule A from PaCas1 (PaCas1_A) and molecule A from AaCas1(AaCas1_A) share 91 equivalent Cα positions that superimpose with anaverage r.m.s.d of 1.28 Å. The color scheme of PaCas1 is consistent withthat in FIG. 1. AaCas1 is colored light green and conserved residues arecolored pink. Similar to the PaCas1 protein, the AaCas1 is a dimercomposed of two molecules with β-domains in distinct orientations,despite having been crystallized under different conditions and in adifferent space group. FIG. 4, Panel B depicts that superposition of theα-helical domains of PaCas1 and AaCas1, as viewed from the perspectiveof the β-strand domain, highlights two structural differences. The twoloops that connect α-helices 10 to 11 and 11 to 12 in PaCas1 are eachreplaced by two finger-like projections in the AaCas1 structure (grayboxes). Alpha-helix 8 (α8) of PaCas1 is positioned horizontally alongthe top and the two molecules are displayed at a 90° rotation about theY-axis. FIG. 4, Panel C illustrates that the β-strand domains of thesetwo molecules share 35 equivalent Cα atoms that superimpose with anaverage r.m.s.d of 1.21 Å. These two molecules are displayed from theperspective of the α-helical domain. β-strands 8 and 9 (gray box) areflipped out of the β-strand domain in molecule A of PaCas1 andpositioned adjacent to α8 (FIG. 4, Panel A). Comparison of molecule Afrom PaCas1 (PaCas1_A) and molecule A from AaCas1 (AaCas1_A) reveals twoprominent structural differences in the α-helical domain (FIG. 4, PanelB). The two short loops that connect α-helix 10 to 11 and 11 to 12 inPaCas1 are each replaced by finger-like projections consisting of twoanti-parallel β-strands (residues 238-255 and 273-286, respectively) inthe AaCas1 structure.

These two Cas1 structures do not share detectable homology with anyother protein structure currently deposited in the protein data bank(PDB).

Example 3 Cas1 Contains a Conserved Divalent Metal Ion Binding Site

To investigate whether Cas1 includes a divalent metal ion bindingsite(s), crystals of the selenomethionine-substituted PaCas1 proteinwere soaked in solutions containing manganese chloride and diffractiondata at the K absorption edge was measured. Anomalous differenceelectron density maps contoured at five sigma revealed eight uniquepeaks, three of which correspond to manganese ions (Mn) in molecules A,B and C, while signal from the other five peaks are fromselenomethionines. Each of these Mn ions, as well as an additional Mnion in molecule D (visible at four sigma), are located in equivalentpositions in the α-helical domains of each molecule and are coordinatedby three conserved residues (Glu190, His254 and Asp286) (FIG. 1).Although the three-dimensional fold of Cas1 is unique, the residuescoordinating the Mn ion are typical among nucleases that employ one ormore metals in their active site. In fact, the chemical environment ofthe Cas1 metal binding site is remarkably similar to the active site ofthe manganese specific endonuclease domain from the cap-snatchingsubunit of the influenza polymerase (Dias et al., 2009).

Although no metal ions were included in the AaCas1 structure, residuesE143, H206 and E221 are located in equivalent positions to the metalbinding residues in the PaCas1 structure (FIGS. 8 and 9). Theconservation of these residues in Cas1 sequences from diverse CASSsubfamilies, as well as their conserved three-dimensional arrangement inthe AaCas1 and PaCas1 structures, suggests a common role for theseresidues in coordinating a metal ion.

Example 4 Cas1 is a Metal-Dependent DNA-Specific Endonuclease

Cas1 nuclease activity was tested by adding PaCas1 to a variety ofnucleic acid substrates including: linear and circular double-strandedDNA (dsDNA: CRISPR2 cloned into pUC19), circular single-stranded DNA(ssDNA: M13 phage), linear double-stranded RNA (dsRNA; in vitrotranscript of CRISPR2) and linear single-stranded RNA (ssRNA; in vitrotranscript of CRISPR2). Cas1 is a metal-dependent DNA-specificendonuclease (FIG. 5). FIG. 5, Panel A depicts that Cas1 nucleaseactivity is restricted to DNA substrates. Lanes 1 and 2 are 1 kb and 100bp DNA ladders, respectively. Lanes 3-6 are dsDNA, lanes 7-10 are ssDNA,lanes 11-14 are dsRNA and lanes 15-18 are ssRNA. The first lane of eachsubstrate type is nucleic acid alone, followed by a lane with nucleicacid and Cas1 in a no metal buffer. The last two lanes of each substratetype include nucleic acid, Cas1 and 2.5 mM Mn²⁺. The last lane of eachsubstrate type was phenol extracted prior to electrophoresis. The dsDNAsubstrate is CRISPR2 from PA14 cloned into pUC19 (pUC19-C2) andlinearized with KpnI (4 Kb). The ssDNA substrate is from M13 phage(reference sequence: NC_003287, 6407nt). RNA substrates are from invitro transcripts of the first 10 repeats and 9 spacers of CRISPR2(568nt). All reactions were incubated at 25° C. for 90 minutes prior toelectrophoresis on a 1.5% agarose gel. Metal-dependent nuclease activityof Cas1 is independent of both sequence and methylation (dam/dcm)pattern (FIG. 5, Panel B). FIG. 5, Panel B shows time course of Cas1nuclease activity on four distinct dsDNA substrates. Lanes 1 and 2 are 1kb and 100 bp DNA ladders, respectively. The 1 kb ladder is the firstlane of each of three subsequent panels. The first panel is pUC19-C2 DNAfrom isolated from methyltransferases (dam⁺/dcm⁺) component E. coli andthe second panel is pUC19-C2 DNA from methyltransferases delete(dam⁻/dcm⁻) E. coli. The third and fourth panels are B3 and DMS3 phageDNA (respectively); each isolated from P. aeruginosa (PA14). The lanesfor each substrate types are: nucleic acid alone, followed by 10, 60 and390 minute incubations with Cas1 in a reaction buffer containing 2.5 mMMn²⁺. The non-sequence specific nuclease activity of Cas1 on circularand linear DNA substrates isolated from E. coli or from P. aeruginosaresults in reaction products that migrate as a non-specific smear onagarose gels (FIG. 5, Panels B, C and D). The average molecular weightof the DNA cleavage products continually decreases over time, resultingin a minimal cleavage product of approximately 80 base pairs inovernight reactions (FIG. 5, Panel C). FIG. 5, Panel C illustrates thetime course of Cas1 nuclease activity on linear dsDNA substrate. Lanes 1and 2 are 1 kb and 100 bp DNA ladders, respectively. Lane 3 islinearized dsDNA alone. Cas1 mediated nuclease reactions (lanes 4-11)were phenol extracted at 1, 15, 30, 60, 90, 120, 240 minutes and at 21hours, prior to electrophoresis. The Cas1 time course is followed by the100 bp and 1 kb DNA ladders, respectively. Cas1 mediated nucleaseactivity is inhibited by EDTA in the last two lanes (30 and 60 minutetime points). FIG. 5, Panel D illustrates that Cas1 is an endonuclease.Lanes 1 and 2 are 1 kb and 100 bp DNA ladders, respectively. Lane 3 iscircular dsDNA alone (CRISPR2 from PA14 cloned into pUC19). Cas1mediated nuclease reactions (lanes 4-6) were phenol extracted at 15, 60,240 minutes prior to electrophoresis. Endonuclease activity of Cas1 isinhibited by EDTA (lanes 7-6). The last two lanes are 100 bp and 1 kbDNA ladders respectively.

Metal ion substitution is a common strategy for understanding the roleof the metal ions in metallonucleases. A panel of metal ion cofactorsincluding alkaline earth metals and transition metals that are commonlyfound in association with metal dependent nucleases were tested fortheir ability to support Cas1 mediated nuclease activity on dsDNAsubstrates. In FIG. 6, Panel A, lanes 1 and 2 are 1 kb and 100 bp DNAladders, respectively. Lane 3 is linear dsDNA alone (CRISPR2 from PA14cloned into pUC19 and linearized with KpnI). Nuclease reactions (lanes4-9) were performed in 100 mM KCl and 20 mM HEPES pH7.5 at 25° C. for 90minutes. Each reaction was supplemented with no metal (NM) or with 2.5mM magnesium (Mg²⁺), manganese (Mn²⁺), cobalt (Co²⁺), calcium (Ca²⁺),iron (Fe²⁺), zinc (Zn²⁺), or EDTA, respectively. Lane 12 is linear dsDNAalone. Lanes 13 and 14 are 100 bp and 1 kb DNA ladders, respectively.All reactions were phenol extracted prior to electrophoresis on a 1.5%agarose gel. Only magnesium (Mg²⁺) and manganese (Mn²⁺) supportCas1-mediated cleavage of dsDNA, and metal preference is dependent onmonovalent salt concentrations (FIG. 6, Panels A and B). In FIG. 6,Panel B lanes 1 and 2 are 1 kb and 100 bp DNA ladders, respectively.Lane 3 is linear dsDNA alone. Lane 4 is linear dsDNA in 100 mM KCl and20 mM HEPES pH7.5. Lanes 5-12 all include Cas1 and linear dsDNA in a 100mM KCl or 10 mM KCl reaction buffer supplemented with no metal (NM) orwith 2.5 mM magnesium (Mg²⁺), manganese (Mn²⁺) or EDTA, respectively.Lanes 13 and 14 are 100 bp and 1 kb DNA ladders, respectively. Althoughmost nucleases exhibit highest activity in the presence of Mg, Cas1 ismore active with Mn²⁺ than with Mg²⁺ at physiological KCl concentrations(FIG. 6, Panel B). Furthermore, Cas1-mediated cleavage of ssDNA, issupported exclusively by Mn²⁺, regardless of KCl concentration (FIG. 6,Panel C). In FIG. 6, Panel C lanes 1 and 2 are 1 kb and 100 bp DNAladders, respectively. Lane 3 is linear ssDNA alone (M13 circularsingle-stranded DNA). Lanes 4-9 all include Cas1 and ssDNA in a 10 mMKCl or 100 mM KCl reaction buffer supplemented with no metal (NM) orwith 2.5 mM magnesium (Mg²⁺), manganese (Mn²⁺) or EDTA, as indicated.Lanes 10 and 11 are 100 bp and 1 kb DNA ladders, respectively.

A series of mutants were constructed to investigate the role ofconserved residues clustered in or around the Cas1 metal-binding pocket.Residues E190, N223, H254, D265 and D268 were mutated to alanine (FIG.7, Panel A). Although each of these mutants was over-expressed, mutationof either E190 or H254 resulted in reduced stability of the protein andwe were unable to purify these two point mutants to homogeneity (FIG.7B). The nuclease activity of the three stable mutants (N223A, D265A andD268A) was tested.

FIG. 7, Panel A shows a close-up of the metal binding pocket in theα-helical domain of molecule A. Anomalous difference electron densitymaps contoured at 5 sigma reveal a manganese ions (green mesh),coordinated by E190, H254 and D268. Asparagine 223 is one of only fouruniversally conserved residues and is the only strictly conservedresidue located outside the metal binding pocket (FIG. 7, Panel A).Asparagine 223 is located at the N-terminal end of α-helix 8, 15.5 Åaway from the metal ion. An alanine substitution at this position(N223A) results in a modest reduction in non-specific nuclease activity(FIG. 7, Panel C). This is in contrast to the potent inhibition ofnuclease activity observed in mutations made within the metal bindingpocket. Mutation of acidic residues in the metal binding pocket atposition 265 (D265A) or at metal coordinating residue 268 (D268A),inhibits non-specific nuclease activity. In FIG. 7, Panel C, the firsttwo lanes are 1 kb and 100 bp DNA ladders, respectively. Lane 3 is dsDNAalone, lanes 4-7 include dsDNA, 2.5 mM Mn²⁺ and one of the followingCas1 proteins in order: wild type Cas1, N223A, D265A and D268A. Allreactions were performed at 25° C. for 90 minutes prior to phenolextraction. Samples were resolved by electrophoresis on a 1.5% agarosegel and stained with ethidium bromide. (*) denotes metal binding mutantsthat inhibit non-specific nuclease activity. In FIG. 7, Panel D the twosubunits of the Cas1 (A-C) homodimer from P. aeruginosa (PA14) aredisplayed as a charge smoothed surface potential (molecule C) and aribbon diagram of (molecule A). Basic residues (blue) cluster around theacidic metal binding pocket (red) creating a positive surface potentialthat may serve to position nucleic acid substrates in proximity to themetal binding site. The Cas1 homodimer is rotated 180° about the Y-axiswith respect to the orientation in FIG. 3.

Thus three independent methods, metal chelation, metal ion substitutionor mutation of metal coordinating residues, all suggest that the metalion is critical for the non-specific degradation of DNA (FIGS. 5, 6 and7, respectively).

The metal ion is located on one exposed face of the α-helical domain. Anextensive cluster of basic residues including R192, K195, R196, K199,R212, K214, R215, K256 R258, R259 and K271 form a positively chargedsurface that spans this face of the α-helical domain and may serve toposition nucleic acid substrate near this metal ion (FIG. 7, Panel D).

Example 5 Identification of a Cas1 Protein Structure from Aquifexaeolicus

FIG. 8, Panel A shows that the Cas1 protein structure from A. aeolicus(AaCas1) consists of two domains, an N-terminal β-strand domain(residues 2-77) and a C-terminal α-helical domain (88-316). The N andC-terminal domains are connected by a linker (77-83) that allows the twodomains to sample different relative orientation. Superimposing residues88-316 from the α-helical domains of molecules A (green) and B (pink) ofAaCas1 (0.59 Å Cα r.m.s.d), reveals differences in domain positioningbetween these two molecules. FIG. 8, Panel B shows that two moleculeswith α-helical and β-strand domains in different orientations form adimer. The dimer interface is mediated by hydrogen bonding betweenβ-strand domains and results in 1,439 Å² of buried surface area.Conserved residues are yellow and the side chains of universallyconserved residues are displayed as sticks with the atoms in each ofthese side chains colored according to red=oxygen, nitrogen=blue andcarbon=gray. The coordinates for this structure were deposited byEbihara, A., Yokoyama, S., and Kuramitsu, S. on Jul. 6, 2007 (PDB:2YZS).

Example 6 Cas1 Sequences Are Diverse

FIG. 9 depicts an alignment of Cas1 sequences from each of the 7 majorCASS subclasses. Theses sequences were aligned by Mcoffee (http://followed by www. followed by tcoffee. followed by org/). Twenty-onesequences, 3 from each of the 7 major CASS subfamilies, are labeled by atwo letter abbreviation of the genus and species, followed by ‘Cas1’,the NCBI gene identification number and the CASS subfamily number 1-7,previously assigned by Makarova et al (2006) (e.g. Pseudomonasaeruginosa, Cas1, NCBI gene identification number: 4380485, from theCASS subfamily 3 is abbreviated as, “PaCas1_4380485_CASS3”). Universallyconserved residues are in red columns and well-conserved residues are inyellow columns.

While the present invention has been described with reference to thespecific embodiments thereof, it should be understood by those skilledin the art that various changes may be made and equivalents may besubstituted without departing from the true spirit and scope of theinvention. In addition, many modifications may be made to adapt aparticular situation, material, composition of matter, process, processstep or steps, to the objective, spirit and scope of the presentinvention. All such modifications are intended to be within the scope ofthe claims appended hereto.

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What is claimed is:
 1. A method of generating nucleic acid fragments ofsubstantially uniform length, the method comprising contacting a DNAsubstrate with a Cas1 polypeptide, wherein said contacting results ingeneration nucleic acid fragments of substantially uniform length. 2.The method of claim 1, wherein the contacting is performed in thepresence of a divalent metal ion.
 3. The method of claim 2, wherein thedivalent metal ion is divalent magnesium ion.
 4. The method of claim 2,wherein the divalent metal ion is divalent manganese ion.
 5. The methodof claim 1, wherein the DNA substrate is inside a cell.
 6. The method ofclaim 1, wherein the DNA substrate is in vitro.
 7. The method of claim1, wherein the DNA substrate is double stranded linear DNA, singlestranded DNA, circular DNA, or genomic DNA.
 8. The method of claim 1,wherein said contacting is for about 0.1 hour to 24 hours.
 9. The methodof claim 1, wherein the nucleic acid fragments are about 30 bp-200 bp inlength.
 10. The method of claim 9, wherein the nucleic acid fragmentsare about 50 bp-100 bp in length.
 11. The method of claim 1, furthercomprising sequencing said nucleic acid fragments.
 12. The method ofclaim 1, wherein the contacting comprises contacting a surfacecomprising a biofilm, wherein the DNA is present in microorganismspresent in the biofilm.
 13. The method of claim 1, wherein thecontacting comprises contacting an epithelial surface of an animal,wherein the DNA is present in the microorganisms present on the surface.14. The method of claim 13, the epithelial surface is mucosal membrane.15. The method of claim 13, the epithelial surface is skin.
 16. Themethod of claim 1, further comprising cloning the nucleic acidfragments.
 17. A kit comprising: a) a purified Cas1 polypeptide; and b)a buffer comprising magnesium or manganese.